1
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Moreno-Córdova EN, Islas-Osuna MA, Contreras-Vergara CA, López-Zavala AA, Ruiz-Bustos E, Reséndiz-Sandoval MG, Castillo-Yañez FJ, Criscitiello MF, Arvizu-Flores AA. Molecular characterization and expression analysis of the chicken-type and goose-type lysozymes from totoaba (Totoaba macdonaldi). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2020; 113:103807. [PMID: 32735961 DOI: 10.1016/j.dci.2020.103807] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 07/23/2020] [Accepted: 07/23/2020] [Indexed: 06/11/2023]
Abstract
Lysozymes play a key role in innate immune response to bacterial pathogens, catalyzing the hydrolysis of the peptidoglycan layer of bacterial cell walls. In this study, the genes encoding the c-type (TmLyzc) and g-type (TmLyzg) lysozymes from Totoaba macdonaldi were cloned and characterized. The cDNA sequences of TmLyzg and TmLyzc were 582 and 432 bp, encoding polypeptides of 193 and 143 amino acids, respectively. Amino acid sequences of these lysozymes shared high identity (60-90%) with their counterparts of other teleosts and showed conserved functional-structural signatures of the lysozyme superfamily. Phylogenetic analysis indicated a close relationship with their vertebrate homologues but distinct evolutionary paths for each lysozyme. Expression analysis by qRT-PCR revealed that TmLyzc was expressed in stomach and pyloric caeca, while TmLyzg was highly expressed in stomach and heart. These results suggest that both lysozymes play important roles in defense of totoaba against bacterial infections or as digestive enzyme.
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Affiliation(s)
- Elena N Moreno-Córdova
- Departamento de Ciencias Químico Biológicas, Universidad de Sonora. Blvd. Rosales S/N, Centro. Hermosillo, SON, CP, 83000, Mexico
| | - María A Islas-Osuna
- Departamento de Tecnología de Alimentos de Origen Vegetal, Centro de Investigación en Alimentación y Desarrollo, Gustavo Enrique Astiazarán Rosas, N0. 46. Hermosillo, SON, CP, 83304, Mexico
| | - Carmen A Contreras-Vergara
- Departamento de Tecnología de Alimentos de Origen Vegetal, Centro de Investigación en Alimentación y Desarrollo, Gustavo Enrique Astiazarán Rosas, N0. 46. Hermosillo, SON, CP, 83304, Mexico
| | - Alonso A López-Zavala
- Departamento de Ciencias Químico Biológicas, Universidad de Sonora. Blvd. Rosales S/N, Centro. Hermosillo, SON, CP, 83000, Mexico
| | - Eduardo Ruiz-Bustos
- Departamento de Ciencias Químico Biológicas, Universidad de Sonora. Blvd. Rosales S/N, Centro. Hermosillo, SON, CP, 83000, Mexico
| | - Mónica G Reséndiz-Sandoval
- Laboratorio de Inmunología, Centro de Investigación en Alimentación y Desarrollo, Gustavo Enrique Astiazarán Rosas, N0. 46. Hermosillo, SON, CP, 83304, Mexico
| | - Francisco J Castillo-Yañez
- Departamento de Ciencias Químico Biológicas, Universidad de Sonora. Blvd. Rosales S/N, Centro. Hermosillo, SON, CP, 83000, Mexico
| | - Michael F Criscitiello
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA; Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M University. Bryan, TX, 77807, USA.
| | - Aldo A Arvizu-Flores
- Departamento de Ciencias Químico Biológicas, Universidad de Sonora. Blvd. Rosales S/N, Centro. Hermosillo, SON, CP, 83000, Mexico.
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2
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Liu X, Rao L, Gennerich A. The regulatory function of the AAA4 ATPase domain of cytoplasmic dynein. Nat Commun 2020; 11:5952. [PMID: 33230227 PMCID: PMC7683685 DOI: 10.1038/s41467-020-19477-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 10/19/2020] [Indexed: 11/08/2022] Open
Abstract
Cytoplasmic dynein is the primary motor for microtubule minus-end-directed transport and is indispensable to eukaryotic cells. Although each motor domain of dynein contains three active AAA+ ATPases (AAA1, 3, and 4), only the functions of AAA1 and 3 are known. Here, we use single-molecule fluorescence and optical tweezers studies to elucidate the role of AAA4 in dynein's mechanochemical cycle. We demonstrate that AAA4 controls the priming stroke of the motion-generating linker, which connects the dimerizing tail of the motor to the AAA+ ring. Before ATP binds to AAA4, dynein remains incapable of generating motion. However, when AAA4 is bound to ATP, the gating of AAA1 by AAA3 prevails and dynein motion can occur. Thus, AAA1, 3, and 4 work together to regulate dynein function. Our work elucidates an essential role for AAA4 in dynein's stepping cycle and underscores the complexity and crosstalk among the motor's multiple AAA+ domains.
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Affiliation(s)
- Xinglei Liu
- Department of Anatomy and Structural Biology and Gruss Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Lu Rao
- Department of Anatomy and Structural Biology and Gruss Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Arne Gennerich
- Department of Anatomy and Structural Biology and Gruss Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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3
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Shi K, Oakland JT, Kurniawan F, Moeller NH, Banerjee S, Aihara H. Structural basis of superinfection exclusion by bacteriophage T4 Spackle. Commun Biol 2020; 3:691. [PMID: 33214665 PMCID: PMC7677548 DOI: 10.1038/s42003-020-01412-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 10/22/2020] [Indexed: 01/21/2023] Open
Abstract
A bacterial cell infected with T4 phage rapidly establishes resistance against further infections by the same or closely related T-even-type bacteriophages – a phenomenon called superinfection exclusion. Here we show that one of the T4 early gene products and a periplasmic protein, Spackle, forms a stoichiometric complex with the lysozyme domain of T4 tail spike protein gp5 and potently inhibits its activity. Crystal structure of the Spackle-gp5 lysozyme complex shows that Spackle binds to a horseshoe-shaped basic patch surrounding the oligosaccharide-binding cleft and induces an allosteric conformational change of the active site. In contrast, Spackle does not appreciably inhibit the lysozyme activity of cytoplasmic T4 endolysin responsible for cell lysis to release progeny phage particles at the final step of the lytic cycle. Our work reveals a unique mode of inhibition for lysozymes, a widespread class of enzymes in biology, and provides a mechanistic understanding of the T4 bacteriophage superinfection exclusion. Ke Shi et al. perform a structural and biochemical characterization of the complex formed between Spackle, an early gene product of T4 and the gp5 lysozyme located in the tail of T4, thereby revealing a new mode of inhibition of the well-known lysozyme enzyme. This study provides structural insight into the phenomenon of superinfection exclusion, phenomenon by which bacterial cells infected with a T4 phage become resistant to secondary infections by the same or closely related phages.
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Affiliation(s)
- Ke Shi
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church Street S.E., Minneapolis, MN, 55455, USA.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Justin T Oakland
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church Street S.E., Minneapolis, MN, 55455, USA.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Fredy Kurniawan
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church Street S.E., Minneapolis, MN, 55455, USA.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Nicholas H Moeller
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church Street S.E., Minneapolis, MN, 55455, USA.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Surajit Banerjee
- Northeastern Collaborative Access Team, Cornell University, Advanced Photon Source, Lemont, IL, 60439, USA
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church Street S.E., Minneapolis, MN, 55455, USA. .,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, 55455, USA.
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4
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Shi K, Kurniawan F, Banerjee S, Moeller NH, Aihara H. Crystal structure of bacteriophage T4 Spackle as determined by native SAD phasing. Acta Crystallogr D Struct Biol 2020; 76:899-904. [PMID: 32876065 PMCID: PMC7466748 DOI: 10.1107/s2059798320010979] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 08/10/2020] [Indexed: 05/05/2023] Open
Abstract
The crystal structure of a bacteriophage T4 early gene product, Spackle, was determined by native sulfur single-wavelength anomalous diffraction (SAD) phasing using synchrotron radiation and was refined to 1.52 Å resolution. The structure shows that Spackle consists of a bundle of five α-helices, forming a relatively flat disc-like overall shape. Although Spackle forms a dimer in the crystal, size-exclusion chromatography with multi-angle light scattering shows that it is monomeric in solution. Mass spectrometry confirms that purified mature Spackle lacks the amino-terminal signal peptide and contains an intramolecular disulfide bond, consistent with its proposed role in the periplasm of T4 phage-infected Escherichia coli cells. The surface electrostatic potential of Spackle shows a strikingly bipolar charge distribution, suggesting a possible mode of membrane association and inhibition of the tail lysozyme activity in T4 bacteriophage superinfection exclusion.
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Affiliation(s)
- Ke Shi
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Fredy Kurniawan
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Surajit Banerjee
- Northeastern Collaborative Access Team, Cornell University, Advanced Photon Source, Lemont, IL 60439, USA
| | - Nicholas H. Moeller
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
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5
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Ignatov M, Kazennov A, Kozakov D. ClusPro FMFT-SAXS: Ultra-fast Filtering Using Small-Angle X-ray Scattering Data in Protein Docking. J Mol Biol 2018; 430:2249-2255. [DOI: 10.1016/j.jmb.2018.03.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 03/08/2018] [Accepted: 03/12/2018] [Indexed: 02/01/2023]
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6
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Abstract
The ClusPro server (https://cluspro.org) is a widely used tool for protein-protein docking. The server provides a simple home page for basic use, requiring only two files in Protein Data Bank (PDB) format. However, ClusPro also offers a number of advanced options to modify the search; these include the removal of unstructured protein regions, application of attraction or repulsion, accounting for pairwise distance restraints, construction of homo-multimers, consideration of small-angle X-ray scattering (SAXS) data, and location of heparin-binding sites. Six different energy functions can be used, depending on the type of protein. Docking with each energy parameter set results in ten models defined by centers of highly populated clusters of low-energy docked structures. This protocol describes the use of the various options, the construction of auxiliary restraints files, the selection of the energy parameters, and the analysis of the results. Although the server is heavily used, runs are generally completed in <4 h.
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7
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Vajda S, Yueh C, Beglov D, Bohnuud T, Mottarella SE, Xia B, Hall DR, Kozakov D. New additions to the ClusPro server motivated by CAPRI. Proteins 2017; 85:435-444. [PMID: 27936493 DOI: 10.1002/prot.25219] [Citation(s) in RCA: 335] [Impact Index Per Article: 47.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Revised: 11/28/2016] [Accepted: 11/29/2016] [Indexed: 12/12/2022]
Abstract
The heavily used protein-protein docking server ClusPro performs three computational steps as follows: (1) rigid body docking, (2) RMSD based clustering of the 1000 lowest energy structures, and (3) the removal of steric clashes by energy minimization. In response to challenges encountered in recent CAPRI targets, we added three new options to ClusPro. These are (1) accounting for small angle X-ray scattering data in docking; (2) considering pairwise interaction data as restraints; and (3) enabling discrimination between biological and crystallographic dimers. In addition, we have developed an extremely fast docking algorithm based on 5D rotational manifold FFT, and an algorithm for docking flexible peptides that include known sequence motifs. We feel that these developments will further improve the utility of ClusPro. However, CAPRI emphasized several shortcomings of the current server, including the problem of selecting the right energy parameters among the five options provided, and the problem of selecting the best models among the 10 generated for each parameter set. In addition, results convinced us that further development is needed for docking homology models. Finally, we discuss the difficulties we have encountered when attempting to develop a refinement algorithm that would be computationally efficient enough for inclusion in a heavily used server. Proteins 2017; 85:435-444. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Sandor Vajda
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, 02215.,Department of Chemistry, Boston University, Boston, Massachusetts, 02215
| | - Christine Yueh
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, 02215
| | - Dmitri Beglov
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, 02215
| | - Tanggis Bohnuud
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, 02215.,Program in Bioinformatics, Boston University, Boston, Massachusetts, 02215
| | - Scott E Mottarella
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, 02215.,Program in Bioinformatics, Boston University, Boston, Massachusetts, 02215
| | - Bing Xia
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, 02215
| | | | - Dima Kozakov
- Department of Applied Mathematics and Statistics, Stony Brook University, New York.,Laufer Center for Physical and Quantitative Biology, Stony Brook University, New York
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8
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Tian L, Hu X, Liu Z, Liu S. Studies on the interaction of heparin with lysozyme by multi-spectroscopic techniques and atomic force microscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2016; 154:27-32. [PMID: 26505285 DOI: 10.1016/j.saa.2015.09.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 08/01/2015] [Accepted: 09/27/2015] [Indexed: 06/05/2023]
Abstract
The interaction between heparin (Hep) and lysozyme (Lyso) in vitro was studied by fluorescence, UV-vis, circular dichroism (CD), resonance Rayleigh scattering (RRS) spectroscopy and atomic force microscopy (AFM) under normal physiological conditions. UV-vis spectra of Lyso showed the absorbance was significantly increased with the addition of Hep. Fluorescence studies revealed that the emission quenching of Lyso with Hep was initiated by static quenching mechanism. CD spectral studies showed that Hep induced conformational changes in the secondary structure of Lyso. RRS spectra of Lyso showed the intensity of scattering was significantly increased with the addition of Hep and the enhanced RRS intensities were proportional to the concentration of Hep in a certain range. Thus, a new RRS method using Lyso as a probe could be used for the determination of Hep. The detection limit for Hep was 3.9 ng mL(-1). In addition, the shape of the complex was characterized by AFM. The possible reaction mechanism and the reasons for the enhancement of RRS intensity had been discussed through experimental results.
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Affiliation(s)
- Lunfu Tian
- Institute of Mechanical Manufacturing Technology, Chinese Academy of Engineering Physics, Mianyang 621900, China; Education Ministry Key Laboratory on Luminescence and Real-Time Analysis, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Xiaoli Hu
- Education Ministry Key Laboratory on Luminescence and Real-Time Analysis, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Zhongfang Liu
- Education Ministry Key Laboratory on Luminescence and Real-Time Analysis, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Shaopu Liu
- Education Ministry Key Laboratory on Luminescence and Real-Time Analysis, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China.
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9
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Xia B, Mamonov A, Leysen S, Allen KN, Strelkov SV, Paschalidis IC, Vajda S, Kozakov D. Accounting for observed small angle X-ray scattering profile in the protein-protein docking server ClusPro. J Comput Chem 2015; 36:1568-72. [PMID: 26095982 DOI: 10.1002/jcc.23952] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 05/06/2015] [Accepted: 05/08/2015] [Indexed: 12/29/2022]
Abstract
The protein-protein docking server ClusPro is used by thousands of laboratories, and models built by the server have been reported in over 300 publications. Although the structures generated by the docking include near-native ones for many proteins, selecting the best model is difficult due to the uncertainty in scoring. Small angle X-ray scattering (SAXS) is an experimental technique for obtaining low resolution structural information in solution. While not sufficient on its own to uniquely predict complex structures, accounting for SAXS data improves the ranking of models and facilitates the identification of the most accurate structure. Although SAXS profiles are currently available only for a small number of complexes, due to its simplicity the method is becoming increasingly popular. Since combining docking with SAXS experiments will provide a viable strategy for fairly high-throughput determination of protein complex structures, the option of using SAXS restraints is added to the ClusPro server. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Bing Xia
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts, 02215
| | - Artem Mamonov
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts, 02215
| | - Seppe Leysen
- Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, 3000, Belgium
| | - Karen N Allen
- Department of Chemistry, Boston University, Boston, Massachusetts, 02215
| | - Sergei V Strelkov
- Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, 3000, Belgium
| | - Ioannis Ch Paschalidis
- Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts, 02215
| | - Sandor Vajda
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts, 02215
| | - Dima Kozakov
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts, 02215
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10
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Liu Z, García-Díaz B, Catacchio B, Chiancone E, Vogel HJ. Protecting Gram-negative bacterial cell envelopes from human lysozyme: Interactions with Ivy inhibitor proteins from Escherichia coli and Pseudomonas aeruginosa. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:3032-46. [PMID: 25838125 DOI: 10.1016/j.bbamem.2015.03.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 03/16/2015] [Accepted: 03/24/2015] [Indexed: 11/15/2022]
Abstract
Lysozymes play an important role in host defense by degrading peptidoglycan in the cell envelopes of pathogenic bacteria. Several Gram-negative bacteria can evade this mechanism by producing periplasmic proteins that inhibit the enzymatic activity of lysozyme. The Escherichia coli inhibitor of vertebrate lysozyme, Ivyc and its Pseudomonas aeruginosa homolog, Ivyp1 have been shown to be potent inhibitors of hen egg white lysozyme (HEWL). Since human lysozyme (HL) plays an important role in the innate immune response, we have examined the binding of HL to Ivyc and Ivyp1. Our results show that Ivyp1 is a weaker inhibitor of HL than Ivyc even though they inhibit HEWL with similar potency. Calorimetry experiments confirm that Ivyp1 interacts more weakly with HL than HEWL. Analytical ultracentrifugation studies revealed that Ivyp1 in solution is a monomer and forms a 30kDa heterodimer with both HL and HEWL, while Ivyc is a homodimer that forms a tetramer with both enzymes. The interaction of Ivyp1 with HL was further characterized by NMR chemical shift perturbation experiments. In addition to the characteristic His-containing Ivy inhibitory loop that binds into the active site of lysozyme, an extended loop (P2) between the final two beta-strands also participates in forming protein-protein interactions. The P2 loop is not conserved in Ivyc and it constitutes a flexible region in Ivyp1 that becomes more rigid in the complex with HL. We conclude that differences in the electrostatic interactions at the binding interface between Ivy inhibitors and distinct lysozymes determine the strength of this interaction. This article is part of a Special Issue entitled: Bacterial Resistance to Antimicrobial Peptides.
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Affiliation(s)
- Zhihong Liu
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Beatriz García-Díaz
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Bruno Catacchio
- Dipartimento di Scienze Biochimiche, Istituto di Biologia e Patologia Molecolari CNR, Università Sapienza, P.le A. Moro, 5-00185 Roma, Italy
| | - Emilia Chiancone
- Dipartimento di Scienze Biochimiche, Istituto di Biologia e Patologia Molecolari CNR, Università Sapienza, P.le A. Moro, 5-00185 Roma, Italy
| | - Hans J Vogel
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada.
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11
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Leysen S, Van Herreweghe JM, Yoneda K, Ogata M, Usui T, Araki T, Michiels CW, Strelkov SV. The structure of the proteinaceous inhibitor PliI from Aeromonas hydrophila in complex with its target lysozyme. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:344-51. [PMID: 25664745 DOI: 10.1107/s1399004714025863] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 11/26/2014] [Indexed: 11/10/2022]
Abstract
Recent microbiological data have revealed that Gram-negative bacteria are able to protect themselves against the lytic action of host lysozymes by secreting proteinaceous inhibitors. Four distinct classes of such inhibitors have been discovered that specifically act against c-type, g-type and i-type lysozymes. Here, the 1.24 Å resolution crystal structure of the periplasmic i-type lysozyme inhibitor from Aeromonas hydrophila (PliI-Ah) in complex with the i-type lysozyme from Meretrix lusoria is reported. The structure is the first to explain the inhibitory mechanism of the PliI family at the atomic level. A distinct `ridge' formed by three exposed PliI loops inserts into the substrate-binding groove of the lysozyme, resulting in a complementary `key-lock' interface. The interface is principally stabilized by the interactions made by the PliI-Ah residues Ser104 and Tyr107 belonging to the conserved SGxY motif, as well as by the other conserved residues Ser46 and Asp76. The functional importance of these residues is confirmed by inhibition assays with the corresponding point mutants of PliI-Ah. The accumulated structural data on lysozyme-inhibitor complexes from several classes indicate that in all cases an extensive interface of either a single or a double `key-lock' type is formed, resulting in highly efficient inhibition. These data provide a basis for the rational development of a new class of antibacterial drugs.
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Affiliation(s)
- Seppe Leysen
- Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium
| | - Joris M Van Herreweghe
- Laboratory of Food Microbiology, Leuven Food Science and Nutrition Research Centre, KU Leuven, 3000 Leuven, Belgium
| | - Kazunari Yoneda
- Department of Bioscience, School of Agriculture, Tokai University, Kawayo, Minamiaso, Kumamoto 869-1404, Japan
| | - Makoto Ogata
- Department of Chemistry and Biochemistry, Fukushima National College of Technology, 30 Nagao, Kamiarakawa, Taira, Iwaki, Fukushima 970-8034, Japan
| | - Taichi Usui
- Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Suruga, Shizuoka 422-8529, Japan
| | - Tomohiro Araki
- Department of Bioscience, School of Agriculture, Tokai University, Kawayo, Minamiaso, Kumamoto 869-1404, Japan
| | - Christiaan W Michiels
- Laboratory of Food Microbiology, Leuven Food Science and Nutrition Research Centre, KU Leuven, 3000 Leuven, Belgium
| | - Sergei V Strelkov
- Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium
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12
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Zhan Y, Zeng W, Jiang G, Wang Q, Shi X, Zhou Z, Deng H, Du Y. Construction of lysozyme exfoliated rectorite-based electrospun nanofibrous membranes for bacterial inhibition. J Appl Polym Sci 2014. [DOI: 10.1002/app.41496] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Yingfei Zhan
- Department of Environmental Science; School of Resource and Environmental Science, Wuhan University; Wuhan 430079 China
- Hubei-MOST KLOS & KLOBME; Wuhan University Stomatological Hospital, Wuhan University; Wuhan 430079 China
| | - Wen Zeng
- Department of Environmental Science; School of Resource and Environmental Science, Wuhan University; Wuhan 430079 China
| | - Guoxia Jiang
- Department of Environmental Science; School of Resource and Environmental Science, Wuhan University; Wuhan 430079 China
| | - Qun Wang
- Department of Chemical and Biological Engineering; Iowa State University; Ames Iowa 50014
- Department of Civil; Construction and Environmental Engineering, Iowa State University; Ames Iowa 50014
| | - Xiaowen Shi
- Department of Environmental Science; School of Resource and Environmental Science, Wuhan University; Wuhan 430079 China
| | - Zhehao Zhou
- Department of Environmental Science; School of Resource and Environmental Science, Wuhan University; Wuhan 430079 China
| | - Hongbing Deng
- Department of Environmental Science; School of Resource and Environmental Science, Wuhan University; Wuhan 430079 China
| | - Yumin Du
- Department of Environmental Science; School of Resource and Environmental Science, Wuhan University; Wuhan 430079 China
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13
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Janin J. The targets of CAPRI rounds 20-27. Proteins 2014; 81:2075-81. [PMID: 23900782 DOI: 10.1002/prot.24375] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 07/12/2013] [Accepted: 07/16/2013] [Indexed: 01/26/2023]
Abstract
Eight CAPRI prediction rounds with a total of 15 targets were held in the years 2010-2012. Only five of the targets were protein assemblies comparable with those of earlier CAPRI rounds. In one target, the solvent positions at the interface had to be predicted; another was a protein-polysaccharide complex. The remainders were designed complexes issued from protein engineering experiments, and the prediction concerned either their structure or the binding affinity of the designed ligand. Affinity prediction was a new experiment in CAPRI, and a challenge for its participants. It pushed the community into developing novel procedures and score functions that will improve the performance of docking methods, help designing binders, and yield better structure-based estimates of the binding free energy of natural assemblies.
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Affiliation(s)
- Joël Janin
- IBBMC, CNRS UMR 8619, Bât. 430, Université Paris-Sud, Orsay, 91405, France
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14
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Lu D, Shang G, Zhang H, Yu Q, Cong X, Yuan J, He F, Zhu C, Zhao Y, Yin K, Chen Y, Hu J, Zhang X, Yuan Z, Xu S, Hu W, Cang H, Gu L. Structural insights into the T6SS effector protein Tse3 and the Tse3-Tsi3 complex fromPseudomonas aeruginosareveal a calcium-dependent membrane-binding mechanism. Mol Microbiol 2014; 92:1092-112. [DOI: 10.1111/mmi.12616] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/10/2014] [Indexed: 12/22/2022]
Affiliation(s)
- Defen Lu
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
- The Liver Centre of Fujian Province; MengChao Hepatobiliary Hospital of Fujian Medical University; Fuzhou 350025 Fujian China
| | - Guijun Shang
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
| | - Heqiao Zhang
- Institute of Biophysics; Chinese Academy of Sciences; Beijing 100101 China
- School of Life Sciences; Tsinghua University; Beijing 100084 China
| | - Qian Yu
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
| | - Xiaoyan Cong
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
| | - Jupeng Yuan
- Institute of Medical Genetics; Shandong University School of Medicine; Jinan 250012 Shandong China
| | - Fengjuan He
- Institute of Medical Genetics; Shandong University School of Medicine; Jinan 250012 Shandong China
| | - Chunyuan Zhu
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
| | - Yanyu Zhao
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
| | - Kun Yin
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
| | - Yuanyuan Chen
- Institute of Biophysics; Chinese Academy of Sciences; Beijing 100101 China
| | - Junqiang Hu
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
| | - Xiaodan Zhang
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
| | - Zenglin Yuan
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
| | - Sujuan Xu
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
| | - Wei Hu
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
| | - Huaixing Cang
- Institute of Biophysics; Chinese Academy of Sciences; Beijing 100101 China
| | - Lichuan Gu
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 Shandong China
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15
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Um SH, Kim JS, Kim K, Kim N, Cho HS, Ha NC. Structural basis for the inhibition of human lysozyme by PliC from Brucella abortus. Biochemistry 2013; 52:9385-93. [PMID: 24308818 DOI: 10.1021/bi401241c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lysozymes are the first line of defense for a diverse range of organisms that catalyze the degradation of bacterial peptidoglycan. Gram-negative bacteria produce proteinaceous lysozyme inhibitors to protect themselves from the action of lysozymes. To date, MliC or PliC (membrane-bound or periplasmic inhibitor of c-type lysozyme, respectively) has been found in various Gram-negative bacteria. Here, we report the crystal structures of Brucella abortus PliC and its complex with human c-type lysozyme. The complex structure demonstrates that the invariant loop of MliC/PliC plays a crucial role in the inhibition of lysozyme via its insertion into the active site cleft of the lysozyme, as previously observed in the complex structure of Pseudomonas aeruginosa MliC and chicken c-type lysozyme. We identified a new binding interface between a loop adjacent to the active site of human lysozyme and a loop carrying Glu112 of B. abortus PliC, the structure of which was disordered in P. aeruginosa MliC. Because MliC/PliC family members have been implicated as putative colonization or virulence factors, the structures and mechanism of action of MliC/PliC will be relevant to the control of bacterial growth in animal hosts.
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Affiliation(s)
- Si-Hyeon Um
- College of Pharmacy and Research Institute for Drug Development, Pusan National University , Busan 609-735, Republic of Korea
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16
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Huang SY, Yan C, Grinter SZ, Chang S, Jiang L, Zou X. Inclusion of the orientational entropic effect and low-resolution experimental information for protein-protein docking in Critical Assessment of PRedicted Interactions (CAPRI). Proteins 2013; 81:2183-91. [PMID: 24227686 PMCID: PMC3916956 DOI: 10.1002/prot.24435] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 09/23/2013] [Accepted: 09/25/2013] [Indexed: 01/20/2023]
Abstract
Inclusion of entropy is important and challenging for protein-protein binding prediction. Here, we present a statistical mechanics-based approach to empirically consider the effect of orientational entropy. Specifically, we globally sample the possible binding orientations based on a simple shape-complementarity scoring function using an FFT-type docking method. Then, for each generated orientation, we calculate the probability through the partition function of the ensemble of accessible states, which are assumed to be represented by the set of nearby binding modes. For each mode, the interaction energy is calculated using our ITScorePP scoring function that was developed in our laboratory based on principles of statistical mechanics. Using the above protocol, we present the results of our participation in Rounds 22-27 of the Critical Assessment of PRedicted Interactions (CAPRI) experiment for 10 targets (T46-T58). Additional experimental information, such as low-resolution small-angle X-ray scattering data, was used when available. In the prediction (or docking) experiments of the 10 target complexes, we achieved correct binding modes for six targets: one with high accuracy (T47), two with medium accuracy (T48 and T57), and three with acceptable accuracy (T49, T50, and T58). In the scoring experiments of seven target complexes, we obtained correct binding modes for six targets: one with high accuracy (T47), two with medium accuracy (T49 and T50), and three with acceptable accuracy (T46, T51, and T53).
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Affiliation(s)
- Sheng-You Huang
- Department of Physics and Astronomy, Department of Biochemistry, Dalton Cardiovascular Research Center, and Informatics Institute, University of Missouri, Columbia, MO 65211
| | | | | | - Shan Chang
- Department of Physics and Astronomy, Department of Biochemistry, Dalton Cardiovascular Research Center, and Informatics Institute, University of Missouri, Columbia, MO 65211
| | - Lin Jiang
- Department of Physics and Astronomy, Department of Biochemistry, Dalton Cardiovascular Research Center, and Informatics Institute, University of Missouri, Columbia, MO 65211
| | - Xiaoqin Zou
- Department of Physics and Astronomy, Department of Biochemistry, Dalton Cardiovascular Research Center, and Informatics Institute, University of Missouri, Columbia, MO 65211
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17
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Qin S, Zhou HX. Using the concept of transient complex for affinity predictions in CAPRI rounds 20-27 and beyond. Proteins 2013; 81:2229-36. [PMID: 23873496 PMCID: PMC3842397 DOI: 10.1002/prot.24366] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 06/26/2013] [Accepted: 06/29/2013] [Indexed: 11/10/2022]
Abstract
Predictions of protein-protein binders and binding affinities have traditionally focused on features pertaining to the native complexes. In developing a computational method for predicting protein-protein association rate constants, we introduced the concept of transient complex after mapping the interaction energy surface. The transient complex is located at the outer boundary of the bound-state energy well, having near-native separation and relative orientation between the subunits but not yet formed most of the short-range native interactions. We found that the width of the binding funnel and the electrostatic interaction energy of the transient complex are among the features predictive of binders and binding affinities. These ideas were very promising for the five affinity-related targets (T43-45, 55, and 56) of CAPRI rounds 20-27. For T43, we ranked the single crystallographic complex as number 1 and were one of only two groups that clearly identified that complex as a true binder; for T44, we ranked the only design with measurable binding affinity as number 4. For the nine docking targets, continuing on our success in previous CAPRI rounds, we produced 10 medium-quality models for T47 and acceptable models for T48 and T49. We conclude that the interaction energy landscape and the transient complex in particular will complement existing features in leading to better prediction of binding affinities.
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Affiliation(s)
- Sanbo Qin
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Huan-Xiang Zhou
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
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18
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Torchala M, Moal IH, Chaleil RAG, Agius R, Bates PA. A Markov-chain model description of binding funnels to enhance the ranking of docked solutions. Proteins 2013; 81:2143-9. [PMID: 23900714 DOI: 10.1002/prot.24369] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 07/03/2013] [Accepted: 07/08/2013] [Indexed: 11/08/2022]
Abstract
Within the crowded, seemingly chaotic environment of the cell, proteins are still able to find their binding partners. This is achieved via an ensemble of trajectories, which funnel them towards their functional binding sites, the binding funnel. Here, we characterize funnel-like energy structures on the global energy landscape using time-homogeneous finite state Markov chain models. These models are based on the idea that transitions can occur between structurally similar docking solutions, with transition probabilities determined by their difference in binding energy. Funnel-like energy structures are those containing solutions with very high equilibrium populations. Although these are found surrounding both near-native and false positive binding sites, we show that the removal of nonfunnel-like energy structures, by filtering away solutions with low maximum equilibrium population, can significantly improve the ranking of docked poses.
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Affiliation(s)
- Mieczyslaw Torchala
- Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, London, WC2A 3LY, United Kingdom
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19
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Kozakov D, Beglov D, Bohnuud T, Mottarella SE, Xia B, Hall DR, Vajda S. How good is automated protein docking? Proteins 2013; 81:2159-66. [PMID: 23996272 DOI: 10.1002/prot.24403] [Citation(s) in RCA: 489] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 08/17/2013] [Accepted: 08/21/2013] [Indexed: 12/12/2022]
Abstract
The protein docking server ClusPro has been participating in critical assessment of prediction of interactions (CAPRI) since its introduction in 2004. This article evaluates the performance of ClusPro 2.0 for targets 46-58 in Rounds 22-27 of CAPRI. The analysis leads to a number of important observations. First, ClusPro reliably yields acceptable or medium accuracy models for targets of moderate difficulty that have also been successfully predicted by other groups, and fails only for targets that have few acceptable models submitted. Second, the quality of automated docking by ClusPro is very close to that of the best human predictor groups, including our own submissions. This is very important, because servers have to submit results within 48 h and the predictions should be reproducible, whereas human predictors have several weeks and can use any type of information. Third, while we refined the ClusPro results for manual submission by running computationally costly Monte Carlo minimization simulations, we observed significant improvement in accuracy only for two of the six complexes correctly predicted by ClusPro. Fourth, new developments, not seen in previous rounds of CAPRI, are that the top ranked model provided by ClusPro was acceptable or better quality for all these six targets, and that the top ranked model was also the highest quality for five of the six, confirming that ranking models based on cluster size can reliably identify the best near-native conformations.
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Affiliation(s)
- Dima Kozakov
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, 02215
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20
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de Vries S, Zacharias M. Flexible docking and refinement with a coarse-grained protein model using ATTRACT. Proteins 2013; 81:2167-74. [PMID: 23996217 DOI: 10.1002/prot.24400] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 07/29/2013] [Accepted: 08/09/2013] [Indexed: 12/13/2022]
Abstract
A coarse-grained (CG) protein model implemented in the ATTRACT protein-protein docking program has been employed to predict protein-protein complex structures in CAPRI Rounds 22-27. For six targets, acceptable or better quality solutions have been submitted corresponding to ~60% of all targets. For one target, promising results on the prediction of the hydration structure at the protein-protein interface have been achieved. New approaches for the rapid flexible refinement have been developed based on a combination of atomistic representation of the bonded geometry and a CG description of nonbonded interactions. Possible further improvements of the docking approach in particular at the scoring and the flexible refinement steps are discussed.
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Affiliation(s)
- Sjoerd de Vries
- Physik-Department T38, Technische Universität München, James Franck Str. 1, 85748, Garching, Germany
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21
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Pallara C, Jiménez-García B, Pérez-Cano L, Romero-Durana M, Solernou A, Grosdidier S, Pons C, Moal IH, Fernandez-Recio J. Expanding the frontiers of protein-protein modeling: from docking and scoring to binding affinity predictions and other challenges. Proteins 2013; 81:2192-200. [PMID: 23934865 DOI: 10.1002/prot.24387] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 07/31/2013] [Accepted: 08/01/2013] [Indexed: 11/06/2022]
Abstract
In addition to protein-protein docking, this CAPRI edition included new challenges, like protein-water and protein-sugar interactions, or the prediction of binding affinities and ΔΔG changes upon mutation. Regarding the standard protein-protein docking cases, our approach, mostly based on the pyDock scheme, submitted correct models as predictors and as scorers for 67% and 57% of the evaluated targets, respectively. In this edition, available information on known interface residues hardly made any difference for our predictions. In one of the targets, the inclusion of available experimental small-angle X-ray scattering (SAXS) data using our pyDockSAXS approach slightly improved the predictions. In addition to the standard protein-protein docking assessment, new challenges were proposed. One of the new problems was predicting the position of the interface water molecules, for which we submitted models with 20% and 43% of the water-mediated native contacts predicted as predictors and scorers, respectively. Another new problem was the prediction of protein-carbohydrate binding, where our submitted model was very close to being acceptable. A set of targets were related to the prediction of binding affinities, in which our pyDock scheme was able to discriminate between natural and designed complexes with area under the curve = 83%. It was also proposed to estimate the effect of point mutations on binding affinity. Our approach, based on machine learning methods, showed high rates of correctly classified mutations for all cases. The overall results were highly rewarding, and show that the field is ready to move forward and face new interesting challenges in interactomics.
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Affiliation(s)
- Chiara Pallara
- Joint BSC-IRB Research Programme in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain
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22
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Rodrigues JPGLM, Melquiond ASJ, Karaca E, Trellet M, van Dijk M, van Zundert GCP, Schmitz C, de Vries SJ, Bordogna A, Bonati L, Kastritis PL, Bonvin AMJJ. Defining the limits of homology modeling in information-driven protein docking. Proteins 2013; 81:2119-28. [PMID: 23913867 DOI: 10.1002/prot.24382] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 07/16/2013] [Accepted: 07/25/2013] [Indexed: 12/28/2022]
Abstract
Information-driven docking is currently one of the most successful approaches to obtain structural models of protein interactions as demonstrated in the latest round of CAPRI. While various experimental and computational techniques can be used to retrieve information about the binding mode, the availability of three-dimensional structures of the interacting partners remains a limiting factor. Fortunately, the wealth of structural information gathered by large-scale initiatives allows for homology-based modeling of a significant fraction of the protein universe. Defining the limits of information-driven docking based on such homology models is therefore highly relevant. Here we show, using previous CAPRI targets, that out of a variety of measures, the global sequence identity between template and target is a simple but reliable predictor of the achievable quality of the docking models. This indicates that a well-defined overall fold is critical for the interaction. Furthermore, the quality of the data at our disposal to characterize the interaction plays a determinant role in the success of the docking. Given reliable interface information we can obtain acceptable predictions even at low global sequence identity. These results, which define the boundaries between trustworthy and unreliable predictions, should guide both experts and nonexperts in defining the limits of what is achievable by docking. This is highly relevant considering that the fraction of the interactome amenable for docking is only bound to grow as the number of experimentally solved structures increases.
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Affiliation(s)
- J P G L M Rodrigues
- Faculty of Science/Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, 3584CH, The Netherlands
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23
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Lensink MF, Wodak SJ. Docking, scoring, and affinity prediction in CAPRI. Proteins 2013; 81:2082-95. [DOI: 10.1002/prot.24428] [Citation(s) in RCA: 199] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 09/12/2013] [Accepted: 09/13/2013] [Indexed: 01/28/2023]
Affiliation(s)
- Marc F. Lensink
- Interdisciplinary Research Institute, USR3078 CNRS; University Lille North of France, Parc de la Haute Borne; 50 avenue de Halley F-59658 Villeneuve d'Ascq cedex France
| | - Shoshana J. Wodak
- Structure and Function Program; Hospital for Sick Children; Toronto Ontario M5G 1X8 Canada
- Department of Biochemistry; University of Toronto; Toronto Ontario Canada
- Department of Molecular Genetics; University of Toronto; Toronto Ontario Canada
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24
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Whitney JC, Chou S, Russell AB, Biboy J, Gardiner TE, Ferrin MA, Brittnacher M, Vollmer W, Mougous JD. Identification, structure, and function of a novel type VI secretion peptidoglycan glycoside hydrolase effector-immunity pair. J Biol Chem 2013; 288:26616-24. [PMID: 23878199 DOI: 10.1074/jbc.m113.488320] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacteria employ type VI secretion systems (T6SSs) to facilitate interactions with prokaryotic and eukaryotic cells. Despite the widespread identification of T6SSs among Gram-negative bacteria, the number of experimentally validated substrate effector proteins mediating these interactions remains small. Here, employing an informatics approach, we define novel families of T6S peptidoglycan glycoside hydrolase effectors. Consistent with the known intercellular self-intoxication exhibited by the T6S pathway, we observe that each effector gene is located adjacent to a hypothetical open reading frame encoding a putative periplasmically localized immunity determinant. To validate our sequence-based approach, we functionally investigate a representative family member from the soil-dwelling bacterium Pseudomonas protegens. We demonstrate that this protein is secreted in a T6SS-dependent manner and that it confers a fitness advantage in growth competition assays with Pseudomonas putida. In addition, we determined the 1.4 Å x-ray crystal structure of this effector in complex with its cognate immunity protein. The structure reveals the effector shares highest overall structural similarity to a glycoside hydrolase family associated with peptidoglycan N-acetylglucosaminidase activity, suggesting that T6S peptidoglycan glycoside hydrolase effector families may comprise significant enzymatic diversity. Our structural analyses also demonstrate that self-intoxication is prevented by the immunity protein through direct occlusion of the effector active site. This work significantly expands our current understanding of T6S effector diversity.
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